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n2:pmcid
PMC0
bibo:doi
10.1038%2Fni.1891
n4:contains
_:vb7958449 _:vb7958456 _:vb7958440
Subject Item
_:vb7958440
rdf:type
n4:Section
dc:title
results
n4:contains
_:vb7958444 _:vb7958445 _:vb7958446 _:vb7958447 _:vb7958441 _:vb7958442 _:vb7958443 _:vb7958448
Subject Item
_:vb7958441
rdf:type
n2:Context
rdf:value
Previous observations have established that the E2A proteins act to modulate lymphocyte differentiation, cell survival, cellular expansion and to suppress the development of lymphoma>>17<<. To determine how the E2A proteins mechanistically coordinate developmental progression and cell growth, E2A occupancy in pre-pro-B (EBF1-deficient) and pro-B cells (RAG1-deficient) was determined using chromatin immunoprecipitation
n2:mentions
n3:19833763
Subject Item
_:vb7958442
rdf:type
n2:Context
rdf:value
Previous studies have demonstrated a tight correlation between transcriptionally active promoters and H3K4 trimethylation, whereas H3K4 monomethylation has been associated with enhancer activity>>2<<–4,18–20. To determine whether E2A occupancy is allied with either promoter or enhancer regions, cell lysates derived from RAG1-deficient pro-B cells were immunoprecipitated with antibodies directed against H3K4me1, H3K4me2 and H3K4me3 and
n2:mentions
n3:18037899 n3:17277777 n3:16122420
Subject Item
_:vb7958443
rdf:type
n2:Context
rdf:value
Previous studies have demonstrated a tight correlation between transcriptionally active promoters and H3K4 trimethylation, whereas H3K4 monomethylation has been associated with enhancer activity2–4,>>18<<–20. To determine whether E2A occupancy is allied with either promoter or enhancer regions, cell lysates derived from RAG1-deficient pro-B cells were immunoprecipitated with antibodies directed against H3K4me1, H3K4me2 and H3K4me3 and
n2:mentions
n3:19212405 n3:19128795 n3:19295514
Subject Item
_:vb7958444
rdf:type
n2:Context
rdf:value
RAG1-deficient pro-B cells were also analyzed separately for global patterns of acetylated H3 (K9 and K14) (ref >>21<<). The majority of E2A binding was associated with H3K4 monomethylation, whereas only a subset was associated with H3 acetylation (Supplementary Fig. 1b).
n2:mentions
n3:18093539
Subject Item
_:vb7958445
rdf:type
n2:Context
rdf:value
and narrow distribution of H3K4 monomethylation as well as a diffuse and asymmetric pattern (Fig. 2c,d). The pattern of H3K4 monomethylation in promoter regions was diffuse for the majority of the segments that were analyzed (Fig. 2d)>>22<<. Focusing on H3K4 monomethylated sites present in pro-B cells, 22% were associated with E2A occupancy (data not shown).
n2:mentions
n3:17512414
Subject Item
_:vb7958446
rdf:type
n2:Context
rdf:value
These data are consistent with genetic data indicating that E2A and EBF1 act synergistically to modulate early B cell development>>11<<.
n2:mentions
n3:10435576
Subject Item
_:vb7958447
rdf:type
n2:Context
rdf:value
We divided the genome into cis-coding elements that show E2A, EBF1 and Foxo1 occupancy, using a computational approach, named Cytoscape>>24<<,25. Putative regulatory targets of E2A were identified based on two criteria. First, genes that showed a significant (≥ 1.5 fold change, P ≤ 0.05) change in transcript abundance between pro-B cells and E2A-deficient pre-pro-B cells were
n2:mentions
n3:14597658
Subject Item
_:vb7958448
rdf:type
n2:Context
rdf:value
We divided the genome into cis-coding elements that show E2A, EBF1 and Foxo1 occupancy, using a computational approach, named Cytoscape24,>>25<<. Putative regulatory targets of E2A were identified based on two criteria. First, genes that showed a significant (≥ 1.5 fold change, P ≤ 0.05) change in transcript abundance between pro-B cells and E2A-deficient pre-pro-B cells were
n2:mentions
n3:15972284
Subject Item
_:vb7958449
rdf:type
n4:Section
dc:title
methods
n4:contains
_:vb7958450 _:vb7958451 _:vb7958452 _:vb7958453 _:vb7958454 _:vb7958455
Subject Item
_:vb7958450
rdf:type
n2:Context
rdf:value
Ebf1−/− hematopoietic progenitors were isolated and grown in the presence of IL-7, SCF and FLT3L as previously described>>6<<. RAG1-deficient pro-B cells were grown in the presence of Opti-MEM, 10% FCS, 2% penicillin/streptomycin and glutamine, 50 µM beta-mercaptoethanol with IL-7 and SCF.
n2:mentions
n3:15030778
Subject Item
_:vb7958451
rdf:type
n2:Context
rdf:value
Retroviral supernatants, containing E47ER or bHLHER control were prepared and transduced into E2A-deficient cell lines as previously described>>6<<. E47-ER and bHLH-ER were activated for 1 h or 6 h with 1 µM tamoxifen and transduced cells were isolated by magnetic selection (Miltenyi) for co-expressed human CD25. For transfection studies reporter constructs were transiently
n2:mentions
n3:15030778
Subject Item
_:vb7958452
rdf:type
n2:Context
rdf:value
The cloning of luciferase constructs was described>>36<<. Dual-luciferase reporter assays were performed as described by the manufacturer (Promega).
n2:mentions
n3:12717431
Subject Item
_:vb7958453
rdf:type
n2:Context
rdf:value
Chromatin immunoprecipitation was performed as described previously>>21<<. Briefly, cells were fixed with 1% formaldehyde for 5 to 20 min at 21°C, lysed and sonicated.
n2:mentions
n3:18093539
Subject Item
_:vb7958454
rdf:type
n2:Context
rdf:value
The network was prepared and analyzed using Cytoscape platform>>24<<. Gene ontology enrichment analysis was performed using Bingo plugin25.
n2:mentions
n3:14597658
Subject Item
_:vb7958455
rdf:type
n2:Context
rdf:value
Gene ontology enrichment analysis was performed using Bingo plugin>>25<<. The significance of the overlap between target sets was calculated based on the Fisher's exact test.
n2:mentions
n3:15972284
Subject Item
_:vb7958456
rdf:type
n4:Section
dc:title
discussion
n4:contains
_:vb7958460 _:vb7958461 _:vb7958462 _:vb7958463 _:vb7958457 _:vb7958458 _:vb7958459 _:vb7958468 _:vb7958469 _:vb7958470 _:vb7958471 _:vb7958464 _:vb7958465 _:vb7958466 _:vb7958467 _:vb7958476 _:vb7958477 _:vb7958478 _:vb7958479 _:vb7958472 _:vb7958473 _:vb7958474 _:vb7958475 _:vb7958480
Subject Item
_:vb7958457
rdf:type
n2:Context
rdf:value
Regulatory networks have been proposed previously that link the activities of E2A, EBF1, PU.1 and Pax5 (refs. >>10<<,26,27). Here we have extended this analysis using genome-wide screens and generated a global network in which the genome has been divided into clusters of genes on the basis of distinct sets of cis-regulatory codes.
n2:mentions
n3:17101802
Subject Item
_:vb7958458
rdf:type
n2:Context
rdf:value
Regulatory networks have been proposed previously that link the activities of E2A, EBF1, PU.1 and Pax5 (refs. 10,>>26<<,27). Here we have extended this analysis using genome-wide screens and generated a global network in which the genome has been divided into clusters of genes on the basis of distinct sets of cis-regulatory codes.
n2:mentions
n3:15469848
Subject Item
_:vb7958459
rdf:type
n2:Context
rdf:value
Regulatory networks have been proposed previously that link the activities of E2A, EBF1, PU.1 and Pax5 (refs. 10,26,>>27<<). Here we have extended this analysis using genome-wide screens and generated a global network in which the genome has been divided into clusters of genes on the basis of distinct sets of cis-regulatory codes.
n2:mentions
n3:16682500
Subject Item
_:vb7958460
rdf:type
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The network shows links between E2A, EBF1 and Pax5, consistent with previous observations>>17<<. The network also includes Foxo1, which until now has not yet been directly connected to other factors, within the context of early B cell development. Based on these as well as previous observations, we propose that E2A activates EBF1
n2:mentions
n3:19833763
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1, then act in concert to induce Pax5 transcription and promote the B cell fate>>9<<.
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Depletion of the LT-HSC and CLP compartments has been observed in both E2A and Foxo1, 2 and 4 triple null mutant mice>>28<<,29,30,31. The roles of E2A and Foxo1 in early B cell development also overlap13,32. At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,34. The marginal versus follicular zone B cell
n2:mentions
n3:17254970
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Depletion of the LT-HSC and CLP compartments has been observed in both E2A and Foxo1, 2 and 4 triple null mutant mice28,>>29<<,30,31. The roles of E2A and Foxo1 in early B cell development also overlap13,32. At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,34. The marginal versus follicular zone B cell fate
n2:mentions
n3:18941177
Subject Item
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Depletion of the LT-HSC and CLP compartments has been observed in both E2A and Foxo1, 2 and 4 triple null mutant mice28,29,>>30<<,31. The roles of E2A and Foxo1 in early B cell development also overlap13,32. At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,34. The marginal versus follicular zone B cell fate
n2:mentions
n3:18674933
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_:vb7958465
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The roles of E2A and Foxo1 in early B cell development also overlap>>13<<,32. At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,34.
n2:mentions
n3:18978794
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The roles of E2A and Foxo1 in early B cell development also overlap13,>>32<<. At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,34.
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n3:9047236
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At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing>>33<<,34. The marginal versus follicular zone B cell fate decision is also modulated by the PI3K and E2A pathways34,35. Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells36,37. In thymocyte
n2:mentions
n3:17277100
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At the immature-B cell compartment both PI3K signaling and E2A play critical roles in receptor editing33,>>34<<. The marginal versus follicular zone B cell fate decision is also modulated by the PI3K and E2A pathways34,35. Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells36,37. In thymocyte
n2:mentions
n3:15078898
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The marginal versus follicular zone B cell fate decision is also modulated by the PI3K and E2A pathways>>34<<,35. Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells36,37. In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint38,39. Finally, PTEN, Foxo and E2A act to prevent the
n2:mentions
n3:15078898
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The marginal versus follicular zone B cell fate decision is also modulated by the PI3K and E2A pathways34,>>35<<. Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells36,37. In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint38,39. Finally, PTEN, Foxo and E2A act to prevent the
n2:mentions
n3:12563260
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Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells>>36<<,37. In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint38,39. Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,41,42. The data described here now provide a mechanism that underpins
n2:mentions
n3:12717431
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Class switch recombination is severely perturbed in both E2A and PTEN-deficient activated B cells36,>>37<<. In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint38,39. Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,41,42. The data described here now provide a mechanism that underpins the
n2:mentions
n3:12615906
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In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint>>38<<,39. Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,41,42.
n2:mentions
n3:14685278
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In thymocyte development both E2A and PTEN enforce the pre-TCR checkpoint38,>>39<<. Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,41,42.
n2:mentions
n3:15452180
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Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma>>39<<,40,41,42. The data described here now provide a mechanism that underpins the linkage between the E2A and FOXO1 proteins: E2A acts immediately upstream of FOXO1 and E2A and FOXO1 are wired together by a wide spectrum of cis-regulatory
n2:mentions
n3:15452180
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Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,>>40<<,41,42. The data described here now provide a mechanism that underpins the linkage between the E2A and FOXO1 proteins: E2A acts immediately upstream of FOXO1 and E2A and FOXO1 are wired together by a wide spectrum of cis-regulatory codes.
n2:mentions
n3:12172006
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Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,>>41<<,42. The data described here now provide a mechanism that underpins the linkage between the E2A and FOXO1 proteins: E2A acts immediately upstream of FOXO1 and E2A and FOXO1 are wired together by a wide spectrum of cis-regulatory codes.
n2:mentions
n3:17254969
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Finally, PTEN, Foxo and E2A act to prevent the development of T cell lymphoma39,40,41,>>42<<. The data described here now provide a mechanism that underpins the linkage between the E2A and FOXO1 proteins: E2A acts immediately upstream of FOXO1 and E2A and FOXO1 are wired together by a wide spectrum of cis-regulatory codes.
n2:mentions
n3:9234734
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LEF mediates Wnt signaling and modulates B cell proliferation>>43<<. Thus, these data raise the interesting possibility that E2A, PI3K and Wnt signaling are connected by LEF to coordinate cell growth and developmental progression.
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Consistent with previous observations, these include genes expressed in alternative lymphoid cell lineages such as CEBPβ, Notch1, RUNX2, RUNX3 and GATA3 >>6<<, 16.
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